Introduction Enzymology

Enzymes are biological molecules which are actually proteins that significantly speed up the rate of virtually all of the chemical reactions that take place within cells. The word enzyme was coined from Greek word “ensymo” meaning   “in yeast”. Essentially all enzymes are proteins but all proteins are not enzymes. They are vital for life and serve a wide range of important functions in the body, such as aiding in digestion and metabolism.  Some enzymes help break large molecules into smaller pieces that are more easily absorbed by the body. Other enzymes help bind two molecules together to produce a new molecule. Enzymes are highly selective catalysts, meaning that each enzyme only speeds up a specific reaction. The molecules that an enzyme works with are called substrates. The substrates bind to a region on the enzyme called the active site.

Enzymology is the study of enzyme kinetics, structure, and function, as well as their relation to each other invivo and invitro.

A catalyst speeds up the rate of a reaction without being changed itself. They are necessary as most biological reactions are very slow.Most enzymes are globular proteins with the exception of a few RNA enzymes (ribozymes). They have an active site made up of a few amino acids. This is where the reaction occurs. The rest of the enzyme acts as a scaffold, bringing these key amino acids together.

The active site forms a cleft or crevice that the substrate can sit in during the reaction. The cleft creates a better environment for the reaction to take place. They may do this, for example, by excluding water.

The active site is almost complementary to the substrate’s shape. Therefore, when the substrate binds, the enzyme must change shape slightly to fit it. This forms the enzyme-substrate complex, also called “ES”. This is the induced fit model, which is an addition to the lock and key hypothesis. Only weak bonds between the enzyme and substrate hold them in place. This is necessary to allow dissociation later on.

Enzymes lower the activation energy, Ea, of a particular reaction. They can do this because they have a high affinity for a transition state. The activation energy is the minimum energy needed for a reaction to occur. Enzymes assist in the reaction so that less energy is needed. This means the reaction can occur more easily. This speeds up the rate of the reaction as it allows the product to be formed faster.

An enzyme has a high affinity for the transition state (even higher than for its substrate). Therefore when the substrate binds, it is quickly forced into the transition state. This is a state that exists between the substrate and the product. The enzyme is said to facilitate the formation of the transition state.

The transition state has a high energy, making it very unstable. It can only exist transiently. The transition state spontaneously turns into the more stable product with lower energy. The enzyme will have a low affinity for the product and so the product is released.

Rate Limiting Steps

The rate limiting step in any reaction is its slowest step. It sets the pace for the entire reaction. After all, a production line can only be as productive as its slowest worker. In enzymatic reactions, the conversion of the enzyme-substrate complex to the product is normally rate limiting. The rate of this step (and therefore the entire enzymatic reaction) is directly proportional to the concentration of ES.

The concentration of ES changes as the reaction progresses. Therefore, the rate of product formation also changes over time. When the reaction reaches equilibrium (steady state) the concentration of ES (and therefore the rate) remains relatively constant.